1
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Grève P, Moumen B, Bouchon D. Three feminizing Wolbachia strains in a single host species: comparative genomics paves the way for identifying sex reversal factors. Front Microbiol 2024; 15:1416057. [PMID: 39238888 PMCID: PMC11376236 DOI: 10.3389/fmicb.2024.1416057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/15/2024] [Indexed: 09/07/2024] Open
Abstract
Introduction Endosymbiotic bacteria in the genus Wolbachia have evolved numerous strategies for manipulating host reproduction in order to promote their own transmission. This includes the feminization of males into functional females, a well-studied phenotype in the isopod Armadillidium vulgare. Despite an early description of this phenotype in isopods and the development of an evolutionary model of host sex determination in the presence of Wolbachia, the underlying genetic mechanisms remain elusive. Methods Here we present the first complete genomes of the three feminizing Wolbachia (wVulC, wVulP, and wVulM) known to date in A. vulgare. These genomes, belonging to Wolbachia B supergroup, contain a large number of mobile elements such as WO prophages with eukaryotic association modules. Taking advantage of these data and those of another Wolbachia-derived feminizing factor integrated into the host genome (f element), we used a comparative genomics approach to identify putative feminizing factors. Results This strategy has enabled us to identify three prophage-associated genes secreted by the Type IV Secretion System: one ankyrin repeat domain-containing protein, one helix-turn-helix transcriptional regulator and one hypothetical protein. In addition, a latrotoxin-related protein, associated with phage relic genes, was shared by all three genomes and the f element. Conclusion These putative feminization-inducing proteins shared canonical interaction features with eukaryotic proteins. These results pave the way for further research into the underlying functional interactions.
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Affiliation(s)
- Pierre Grève
- Université de Poitiers, Ecologie et Biologie des Interactions, UMR CNRS 7267, Poitiers, France
| | - Bouziane Moumen
- Université de Poitiers, Ecologie et Biologie des Interactions, UMR CNRS 7267, Poitiers, France
| | - Didier Bouchon
- Université de Poitiers, Ecologie et Biologie des Interactions, UMR CNRS 7267, Poitiers, France
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2
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Tan Y, Aravind L, Zhang D. Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia. Genome Biol Evol 2024; 16:evae171. [PMID: 39106433 PMCID: PMC11342252 DOI: 10.1093/gbe/evae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024] Open
Abstract
Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
- Program of Bioinformatics and Computational Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO 63103, USA
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3
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Hopper KR, Wang X, Kenis M, Seehausen ML, Abram PK, Daane KM, Buffington ML, Hoelmer KA, Kingham BF, Shevchenko O, Bernberg E. Genome divergence and reproductive incompatibility among populations of Ganaspis near brasiliensis. G3 (BETHESDA, MD.) 2024; 14:jkae090. [PMID: 38718200 PMCID: PMC11228843 DOI: 10.1093/g3journal/jkae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/12/2024] [Indexed: 07/09/2024]
Abstract
During the last decade, the spotted wing drosophila, Drosophila suzukii, has spread from eastern Asia to the Americas, Europe, and Africa. This fly attacks many species of cultivated and wild fruits with soft, thin skins, where its serrated ovipositor allows it to lay eggs in undamaged fruit. Parasitoids from the native range of D. suzukii may provide sustainable management of this polyphagous pest. Among these parasitoids, host-specificity testing has revealed a lineage of Ganaspis near brasiliensis, referred to in this paper as G1, that appears to be a cryptic species more host-specific to D. suzukii than other parasitoids. Differentiation among cryptic species is critical for introduction and subsequent evaluation of their impact on D. suzukii. Here, we present results on divergence in genomic sequences and architecture and reproductive isolation between lineages of Ganaspis near brasiliensis that appear to be cryptic species. We studied five populations, two from China, two from Japan, and one from Canada, identified as the G1 vs G3 lineages based on differences in cytochrome oxidase l sequences. We assembled and annotated the genomes of these populations and analyzed divergences in sequence and genome architecture between them. We also report results from crosses to test reproductive compatibility between the G3 lineage from China and the G1 lineage from Japan. The combined results on sequence divergence, differences in genome architectures, ortholog divergence, reproductive incompatibility, differences in host ranges and microhabitat preferences, and differences in morphology show that these lineages are different species. Thus, the decision to evaluate the lineages separately and only import and introduce the more host-specific lineage to North America and Europe was appropriate.
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Affiliation(s)
- Keith R Hopper
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Marc Kenis
- CABI, Rue des Grillons 1, CH-2800 Delémont, Switzerland
| | | | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, 6947 Highway 7, PO Box 1000, Agassiz, BC V0 M 1A2, Canada
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720-3114, USA
| | - Matthew L Buffington
- United States Department of Agriculture, Agricultural Research Service, Washington, c/o Smithsonian Institution, National Museum of Natural History, 10th and Constitution NW, MRC-168, Washington, DC 20013-7012, USA
| | - Kim A Hoelmer
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Olga Shevchenko
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Erin Bernberg
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
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4
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Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mixed Wolbachia infections resolve rapidly during in vitro evolution. PLoS Pathog 2024; 20:e1012149. [PMID: 39052691 DOI: 10.1371/journal.ppat.1012149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/06/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between the two strains in cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.
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Affiliation(s)
- Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Pingting Wang
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Maximilian Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, United States of America
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America
| | - William T Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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5
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Łukasik P, Kolasa MR. With a little help from my friends: the roles of microbial symbionts in insect populations and communities. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230122. [PMID: 38705185 PMCID: PMC11070262 DOI: 10.1098/rstb.2023.0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/14/2023] [Indexed: 05/07/2024] Open
Abstract
To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał R. Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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6
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Ferguson LF, Ross PA, van Heerwaarden B. Wolbachia infection negatively impacts Drosophila simulans heat tolerance in a strain- and trait-specific manner. Environ Microbiol 2024; 26:e16609. [PMID: 38558489 DOI: 10.1111/1462-2920.16609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
The susceptibility of insects to rising temperatures has largely been measured by their ability to survive thermal extremes. However, the capacity for maternally inherited endosymbionts to influence insect heat tolerance has been overlooked. Further, while some studies have addressed the impact of heat on traits like fertility, which can decline at temperatures below lethal thermal limits, none have considered the impact of endosymbionts. Here, we assess the impact of three Wolbachia strains (wRi, wAu and wNo) on the survival and fertility of Drosophila simulans exposed to heat stress during development or as adults. The effect of Wolbachia infection on heat tolerance was generally small and trait/strain specific. Only the wNo infection significantly reduced the survival of adult males after a heat shock. When exposed to fluctuating heat stress during development, the wRi and wAu strains reduced egg-to-adult survival but only the wNo infection reduced male fertility. Wolbachia densities of all three strains decreased under developmental heat stress, but reductions occurred at temperatures above those that reduced host fertility. These findings emphasize the necessity to account for endosymbionts and their effect on both survival and fertility when investigating insect responses to heat stress.
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Affiliation(s)
- Liam F Ferguson
- School of BioSciences, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Perran A Ross
- School of BioSciences, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- Section for Bioscience and Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Belinda van Heerwaarden
- School of BioSciences, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
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7
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Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mixed Wolbachia infections resolve rapidly during in vitro evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586911. [PMID: 38585949 PMCID: PMC10996604 DOI: 10.1101/2024.03.27.586911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species, tissues, and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.
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Affiliation(s)
- Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Pingting Wang
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Maximilian Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, USA
| | - William T Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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8
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Konecka E, Szymkowiak P. Wolbachia supergroup A in Enoplognatha latimana (Araneae: Theridiidae) in Poland as an example of possible horizontal transfer of bacteria. Sci Rep 2024; 14:7486. [PMID: 38553514 PMCID: PMC10980700 DOI: 10.1038/s41598-024-57701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Wolbachia (phylum Pseudomonadota, class Alfaproteobacteria, order Rickettsiales, family Ehrlichiaceae) is a maternally inherited bacterial symbiont infecting more than half of arthropod species worldwide and constituting an important force in the evolution, biology, and ecology of invertebrate hosts. Our study contributes to the limited knowledge regarding the presence of intracellular symbiotic bacteria in spiders. Specifically, we investigated the occurrence of Wolbachia infection in the spider species Enoplognatha latimana Hippa and Oksala, 1982 (Araneae: Theridiidae) using a sample collected in north-western Poland. To the best of our knowledge, this is the first report of Wolbachia infection in E. latimana. A phylogeny based on the sequence analysis of multiple genes, including 16S rRNA, coxA, fbpA, ftsZ, gatB, gltA, groEL, hcpA, and wsp revealed that Wolbachia from the spider represented supergroup A and was related to bacterial endosymbionts discovered in other spider hosts, as well as insects of the orders Diptera and Hymenoptera. A sequence unique for Wolbachia supergroup A was detected for the ftsZ gene. The sequences of Wolbachia housekeeping genes have been deposited in publicly available databases and are an important source of molecular data for comparative studies. The etiology of Wolbachia infection in E. latimana is discussed.
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Affiliation(s)
- Edyta Konecka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Paweł Szymkowiak
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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9
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Hyder M, Lodhi AM, Wang Z, Bukero A, Gao J, Mao R. Wolbachia Interactions with Diverse Insect Hosts: From Reproductive Modulations to Sustainable Pest Management Strategies. BIOLOGY 2024; 13:151. [PMID: 38534421 DOI: 10.3390/biology13030151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Effective in a variety of insect orders, including dipteran, lepidopteran, and hemipteran, Wolbachia-based control tactics are investigated, noting the importance of sterile and incompatible insect techniques. Encouraging approaches for controlling Aedes mosquitoes are necessary, as demonstrated by the evaluation of a new SIT/IIT combination and the incorporation of SIT into Drosophila suzukii management. For example, Wolbachia may protect plants from rice pests, demonstrating its potential for agricultural biological vector management. Maternal transmission and cytoplasmic incompatibility dynamics are explored, while Wolbachia phenotypic impacts on mosquito and rice pest management are examined. The importance of host evolutionary distance is emphasised in recent scale insect research that addresses host-shifting. Using greater information, a suggested method for comprehending Wolbachia host variations in various contexts emphasises ecological connectivity. Endosymbionts passed on maternally in nematodes and arthropods, Wolbachia are widely distributed around the world and have evolved both mutualistic and parasitic traits. Wolbachia is positioned as a paradigm for microbial symbiosis due to advancements in multiomics, gene functional assays, and its effect on human health. The challenges and opportunities facing Wolbachia research include scale issues, ecological implications, ethical conundrums, and the possibility of customising strains through genetic engineering. It is thought that cooperative efforts are required to include Wolbachia-based therapies into pest management techniques while ensuring responsible and sustainable ways.
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Affiliation(s)
- Moazam Hyder
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Abdul Mubeen Lodhi
- Department Plant Protection, Sindh Agriculture University, Tandojam 70080, Pakistan
| | - Zhaohong Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Aslam Bukero
- Department of Entomology, Sindh Agriculture University, Tandojam 70080, Pakistan
| | - Jing Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Runqian Mao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
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10
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Pramono AK, Hidayanti AK, Tagami Y, Ando H. Bacterial community and genome analysis of cytoplasmic incompatibility-inducing Wolbachia in American serpentine leafminer, Liriomyza trifolii. Front Microbiol 2024; 15:1304401. [PMID: 38380092 PMCID: PMC10877061 DOI: 10.3389/fmicb.2024.1304401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/12/2024] [Indexed: 02/22/2024] Open
Abstract
Liriomyza trifolii, an agricultural pest, is occasionally infected by Wolbachia. A Wolbachia strain present in Liriomyza trifolii is associated with cytoplasmic incompatibility (CI) effects, leading to the death of embryos resulting from incompatible crosses between antibiotic-treated or naturally Wolbachia-free strain females and Wolbachia-infected males. In this study, high-throughput sequencing of hypervariable rRNA genes was employed to characterize the bacterial community in Wolbachia-infected L. trifolii without antibiotic treatment. The analysis revealed that Wolbachia dominates the bacterial community in L. trifolii, with minor presence of Acinetobacter, Pseudomonas, and Limnobacter. To elucidate the genetic basis of the CI phenotype, metagenomic sequencing was also conducted to assemble the genome of the Wolbachia strain. The draft-genome of the Wolbachia strain wLtri was 1.35 Mbp with 34% GC content and contained 1,487 predicted genes. Notably, within the wLtri genome, there are three distinct types of cytoplasmic incompatibility factor (cif) genes: Type I, Type III, and Type V cifA;B. These genes are likely responsible for inducing the strong cytoplasmic incompatibility observed in L. trifolii.
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Affiliation(s)
- Ajeng K. Pramono
- Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Ardhiani K. Hidayanti
- School of Biological Environment, The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
- School of Life Sciences and Technology, Institut Teknologi Bandung (ITB), Bandung, Indonesia
| | - Yohsuke Tagami
- Laboratory of Applied Entomology, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hiroki Ando
- Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University, Gifu, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Japan
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11
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Trouche B, Schrieke H, Duron O, Eren AM, Reveillaud J. Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms. ISME COMMUNICATIONS 2024; 4:ycae078. [PMID: 38915450 PMCID: PMC11195471 DOI: 10.1093/ismeco/ycae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.
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Affiliation(s)
- Blandine Trouche
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Hans Schrieke
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Olivier Duron
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA 02543, United States
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, 26129 Oldenburg, Germany
| | - Julie Reveillaud
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
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12
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Valerio F, Twort VG, Duplouy A. Screening Host Genomic Data for Wolbachia Infections. Methods Mol Biol 2024; 2739:251-274. [PMID: 38006557 DOI: 10.1007/978-1-0716-3553-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Less than a decade ago, the production of Wolbachia genomic assemblies was tedious, time-consuming, and expensive. The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. However, as an endosymbiotic bacterium, Wolbachia does not grow outside the host cell environment, and large-scale recovery of the bacteria required mass rearing of their host, preferably clones of a single individual to avoid strain genetic diversity, or amplification of cell cultures infected with a single Wolbachia strain. Bacterial DNA could be separated from host DNA based on genomic size. Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. We hope this simple protocol will support many projects aiming at studying diverse Wolbachia genome assemblies.
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Affiliation(s)
- Federica Valerio
- Insect Symbiosis Ecology and Evolution, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Changes, University of Helsinki, Helsinki, Finland
| | - Victoria G Twort
- The Finnish Museum of Natural History, Luomus, University of Helsinki, Helsinki, Finland
| | - Anne Duplouy
- Insect Symbiosis Ecology and Evolution, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Research Centre for Ecological Changes, University of Helsinki, Helsinki, Finland.
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13
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Kaur A, Brown AMV. Detection and Analysis of Wolbachia in Plant-Parasitic Nematodes and Insights into Wolbachia Evolution. Methods Mol Biol 2024; 2739:115-134. [PMID: 38006548 DOI: 10.1007/978-1-0716-3553-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Since the discovery of Wolbachia in plant-parasitic nematodes (PPNs), there has been increased interest in this earliest branching clade that may hold important clues to early transitions in Wolbachia function in the Ecdysozoa. However, due to the specialized skills and equipment of nematology and the difficulty in culturing most PPNs, these PPN-type Wolbachia remain undersampled and poorly understood. To date, there are few established laboratory methods for working with PPN-type Wolbachia strains, and most research has relied on chance discovery and comparative genomics. Here, we address this challenge by providing detailed methods to assist researchers with more efficiently collecting PPNs and screen these communities, populations, or single nematodes with a newly developed PPN-type Wolbachia-specific PCR assay. We provide an overview of the typical yields and outcomes of these methods, to facilitate further targeted cultivation or experimental methods, and finally we provide a short introduction to some of the specific challenges and solutions in following through with comparative or population genomics on PPN-type Wolbachia strains.
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Affiliation(s)
- Amandeep Kaur
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
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14
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Heeren S, Maes I, Sanders M, Lye LF, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, Van den Broeck F. Diversity and dissemination of viruses in pathogenic protozoa. Nat Commun 2023; 14:8343. [PMID: 38102141 PMCID: PMC10724245 DOI: 10.1038/s41467-023-44085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis and their dsRNA Leishmania virus 1. We show that parasite populations circulate in tropical rainforests and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites are geographically and ecologically more dispersed and associated with an increased prevalence, diversity and spread of viruses. Our results suggest that parasite gene flow and hybridization increased the frequency of parasite-virus symbioses, a process that may change the epidemiology of leishmaniasis in the region.
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Affiliation(s)
- Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanessa Adaui
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James A Cotton
- Welcome Sanger Institute, Hinxton, UK
- School of Biodiversity, One Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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15
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Shapoval NA, Kir’yanov AV, Krupitsky AV, Yakovlev RV, Romanovich AE, Zhang J, Cong Q, Grishin NV, Kovalenko MG, Shapoval GN. Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection. INSECTS 2023; 14:943. [PMID: 38132616 PMCID: PMC10743618 DOI: 10.3390/insects14120943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
The genus Colias Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar Colias species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question. We recover and include in our analysis DNA barcodes of the century-old type specimens, the lectotype of C. tamerlana deposited in the Natural History Museum (Museum für Naturkunde), Berlin, Germany (ZMHU) and the paralectotype of C. tamerlana and the lectotype of C. mongola deposited in the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP). Our analysis grouped all specimens within four (HP_I-HP_IV) deeply divergent but geographically poorly structured clades which did not support nonconspecifity of C. mongola-C. tamerlana. We also show that all studied females of the widely distributed haplogroup HP_II were infected with a single Wolbachia strain belonging to the supergroup B, while the males of this haplogroup, as well as all other investigated specimens of both sexes, were not infected. Our data highlight the relevance of large-scale sampling dataset analysis and the need for testing for Wolbachia infection to avoid erroneous phylogenetic reconstructions and species misidentification.
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Affiliation(s)
- Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia
| | - Alexander V. Kir’yanov
- Photonics Department, Centro de Investigaciones en Optica, Lomas del Bosque 115, Leon 37150, Mexico;
| | - Anatoly V. Krupitsky
- Department of Entomology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, GSP-1, korp. 12, 119991 Moscow, Russia;
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Pr. 33, 119071 Moscow, Russia
| | - Roman V. Yakovlev
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
- Institute of Biology, Tomsk State University, Lenina Pr. 36, 634050 Tomsk, Russia
| | - Anna E. Romanovich
- Resource Center for Development of Molecular and Cellular Technologies, St. Petersburg State University, Universitetskaya Nab., 7/9, 199034 St. Petersburg, Russia;
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Margarita G. Kovalenko
- Research and Methodological Department of Entomology, All-Russian Plant Quarantine Center, Pogranichnaya 32, 140150 Bykovo, Russia;
| | - Galina N. Shapoval
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
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16
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Patel V, Lynn-Bell N, Chevignon G, Kucuk RA, Higashi CHV, Carpenter M, Russell JA, Oliver KM. Mobile elements create strain-level variation in the services conferred by an aphid symbiont. Environ Microbiol 2023; 25:3333-3348. [PMID: 37864320 DOI: 10.1111/1462-2920.16520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/27/2023] [Indexed: 10/22/2023]
Abstract
Heritable, facultative symbionts are common in arthropods, often functioning in host defence. Despite moderately reduced genomes, facultative symbionts retain evolutionary potential through mobile genetic elements (MGEs). MGEs form the primary basis of strain-level variation in genome content and architecture, and often correlate with variability in symbiont-mediated phenotypes. In pea aphids (Acyrthosiphon pisum), strain-level variation in the type of toxin-encoding bacteriophages (APSEs) carried by the bacterium Hamiltonella defensa correlates with strength of defence against parasitoids. However, co-inheritance creates difficulties for partitioning their relative contributions to aphid defence. Here we identified isolates of H. defensa that were nearly identical except for APSE type. When holding H. defensa genotype constant, protection levels corresponded to APSE virulence module type. Results further indicated that APSEs move repeatedly within some H. defensa clades providing a mechanism for rapid evolution in anti-parasitoid defences. Strain variation in H. defensa also correlates with the presence of a second symbiont Fukatsuia symbiotica. Predictions that nutritional interactions structured this coinfection were not supported by comparative genomics, but bacteriocin-containing plasmids unique to co-infecting strains may contribute to their common pairing. In conclusion, strain diversity, and joint capacities for horizontal transfer of MGEs and symbionts, are emergent players in the rapid evolution of arthropods.
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Affiliation(s)
- Vilas Patel
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Nicole Lynn-Bell
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Germain Chevignon
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER, La Tremblade, France
| | - Roy A Kucuk
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | | | - Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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17
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Strunov A, Kirchner S, Schindelar J, Kruckenhauser L, Haring E, Kapun M. Historic Museum Samples Provide Evidence for a Recent Replacement of Wolbachia Types in European Drosophila melanogaster. Mol Biol Evol 2023; 40:msad258. [PMID: 37995370 PMCID: PMC10701101 DOI: 10.1093/molbev/msad258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host-symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster, which is naturally infected with at least 5 different variants among which wMel and wMelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that wMelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant wMel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90 to 200 yr ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host-symbiont interactions. However, we also identified contamination with DNA from crickets that resulted in co-contamination with cricket-specific Wolbachia in several samples. These results underpin the need for rigorous quality assessments of museomic data sets to account for contamination as a source of error that may strongly influence biological interpretations if it remains undetected.
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Affiliation(s)
- Anton Strunov
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sandra Kirchner
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Julia Schindelar
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Luise Kruckenhauser
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
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18
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An Y, Braga MP, Garcia SL, Grudzinska-Sterno M, Hambäck PA. Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles. MICROBIAL ECOLOGY 2023; 86:2477-2487. [PMID: 37314477 PMCID: PMC10640405 DOI: 10.1007/s00248-023-02251-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/27/2023] [Indexed: 06/15/2023]
Abstract
Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.
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Affiliation(s)
- Yueqing An
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
| | - Mariana P Braga
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Helsinki Life Science Institute, University of Helsinki, Helsinki, Finland
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | | | - Peter A Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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19
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Guo Y, Shao J, Wu Y, Li Y. Using Wolbachia to control rice planthopper populations: progress and challenges. Front Microbiol 2023; 14:1244239. [PMID: 37779725 PMCID: PMC10537216 DOI: 10.3389/fmicb.2023.1244239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Wolbachia have been developed as a tool for protecting humans from mosquito populations and mosquito-borne diseases. The success of using Wolbachia relies on the facts that Wolbachia are maternally transmitted and that Wolbachia-induced cytoplasmic incompatibility provides a selective advantage to infected over uninfected females, ensuring that Wolbachia rapidly spread through the target pest population. Most transinfected Wolbachia exhibit a strong antiviral response in novel hosts, thus making it an extremely efficient technique. Although Wolbachia has only been used to control mosquitoes so far, great progress has been made in developing Wolbachia-based approaches to protect plants from rice pests and their associated diseases. Here, we synthesize the current knowledge about the important phenotypic effects of Wolbachia used to control mosquito populations and the literature on the interactions between Wolbachia and rice pest planthoppers. Our aim is to link findings from Wolbachia-mediated mosquito control programs to possible applications in planthoppers.
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Affiliation(s)
| | | | | | - Yifeng Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangzhou, China
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20
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Medina P, Russell SL, Corbett-Detig R. Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species. PLoS One 2023; 18:e0288261. [PMID: 37432953 DOI: 10.1371/journal.pone.0288261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.
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Affiliation(s)
- Paloma Medina
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
| | - Shelbi L Russell
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
| | - Russell Corbett-Detig
- Genomics Institute, Department of Biomolecular Engineering UC Santa Cruz, Santa Cruz, CA, United States of America
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21
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Fiutek N, Couger MB, Pirro S, Roy SW, de la Torre JR, Connor EF. Genomic Assessment of the Contribution of the Wolbachia Endosymbiont of Eurosta solidaginis to Gall Induction. Int J Mol Sci 2023; 24:ijms24119613. [PMID: 37298563 DOI: 10.3390/ijms24119613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.
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Affiliation(s)
- Natalie Fiutek
- Department of Biology, San Francisco State University, San Francisco, CA 94112, USA
| | - Matthew B Couger
- Department of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stacy Pirro
- Iridian Genomes Inc., Bethesda, MD 20817, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, CA 94112, USA
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA 94112, USA
| | - Edward F Connor
- Department of Biology, San Francisco State University, San Francisco, CA 94112, USA
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22
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Mioduchowska M, Konecka E, Gołdyn B, Pinceel T, Brendonck L, Lukić D, Kaczmarek Ł, Namiotko T, Zając K, Zając T, Jastrzębski JP, Bartoszek K. Playing Peekaboo with a Master Manipulator: Metagenetic Detection and Phylogenetic Analysis of Wolbachia Supergroups in Freshwater Invertebrates. Int J Mol Sci 2023; 24:ijms24119400. [PMID: 37298356 DOI: 10.3390/ijms24119400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The infamous "master manipulators"-intracellular bacteria of the genus Wolbachia-infect a broad range of phylogenetically diverse invertebrate hosts in terrestrial ecosystems. Wolbachia has an important impact on the ecology and evolution of their host with documented effects including induced parthenogenesis, male killing, feminization, and cytoplasmic incompatibility. Nonetheless, data on Wolbachia infections in non-terrestrial invertebrates are scarce. Sampling bias and methodological limitations are some of the reasons limiting the detection of these bacteria in aquatic organisms. In this study, we present a new metagenetic method for detecting the co-occurrence of different Wolbachia strains in freshwater invertebrates host species, i.e., freshwater Arthropoda (Crustacea), Mollusca (Bivalvia), and water bears (Tardigrada) by applying NGS primers designed by us and a Python script that allows the identification of Wolbachia target sequences from the microbiome communities. We also compare the results obtained using the commonly applied NGS primers and the Sanger sequencing approach. Finally, we describe three supergroups of Wolbachia: (i) a new supergroup V identified in Crustacea and Bivalvia hosts; (ii) supergroup A identified in Crustacea, Bivalvia, and Eutardigrada hosts, and (iii) supergroup E infection in the Crustacea host microbiome community.
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Affiliation(s)
- Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdańsk, Poland
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Poland
- Department of Marine Plankton Research, Institute of Oceanography, University of Gdansk, 81-378 Gdynia, Poland
| | - Edyta Konecka
- Department of Microbiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Bartłomiej Gołdyn
- Department of General Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Tom Pinceel
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, 3000 Leuven, Belgium
- Centre for Environmental Management, University of the Free State, Potchefstroom 2520, South Africa
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Luc Brendonck
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, 3000 Leuven, Belgium
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa
| | - Dunja Lukić
- Department of Wetland Ecology, Estación Biológica de Doñana-CSIC, 41092 Sevilla, Spain
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznań, Poland
| | - Tadeusz Namiotko
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdańsk, Poland
| | - Katarzyna Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Kraków, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Kraków, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Division of Statistics and Machine Learning, Linköping University, SE-581 83 Linköping, Sweden
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23
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Moore LD, Ballinger MJ. The toxins of vertically transmitted Spiroplasma. Front Microbiol 2023; 14:1148263. [PMID: 37275155 PMCID: PMC10232968 DOI: 10.3389/fmicb.2023.1148263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/19/2023] [Indexed: 06/07/2023] Open
Abstract
Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor symbiont persistence in host populations. In Spiroplasma, these phenotypes have been linked to toxin and virulence domains among a few related strains. However, these domains also appear frequently in phylogenetically distant Spiroplasma, and little is known about their distribution across the Spiroplasma genus. In this study, we present the complete genome sequence of the Spiroplasma symbiont of Drosophila atripex, a non-manipulating member of the Ixodetis clade of Spiroplasma, for which genomic data are still limited. We perform a genus-wide comparative analysis of toxin domains implicated in defensive and reproductive phenotypes. From 12 VT and 31 non-VT Spiroplasma genomes, ribosome-inactivating proteins (RIPs), OTU-like cysteine proteases (OTUs), ankyrins, and ETX/MTX2 domains show high propensity for VT Spiroplasma compared to non-VT Spiroplasma. Specifically, OTU and ankyrin domains can be found only in VT-Spiroplasma, and RIP domains are found in all VT Spiroplasma and three non-VT Spiroplasma. These domains are frequently associated with Spiroplasma plasmids, suggesting a possible mechanism for dispersal and maintenance among heritable strains. Searching insect genome assemblies available on public databases uncovered uncharacterized Spiroplasma genomes from which we identified several spaid-like genes encoding RIP, OTU, and ankyrin domains, suggesting functional interactions among those domain types. Our results suggest a conserved core of symbiont domains play an important role in the evolution and persistence of VT Spiroplasma in insects.
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Affiliation(s)
- Logan D. Moore
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
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24
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Rodrigues J, Lefoulon E, Gavotte L, Perillat-Sanguinet M, Makepeace B, Martin C, D'Haese CA. Wolbachia springs eternal: symbiosis in Collembola is associated with host ecology. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230288. [PMID: 37266040 PMCID: PMC10230187 DOI: 10.1098/rsos.230288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Wolbachia are endosymbiotic alpha-proteobacteria infecting a wide range of arthropods and nematode hosts with diverse interactions, from reproductive parasites to obligate mutualists. Their taxonomy is defined by lineages called supergroups (labelled by letters of the alphabet), while their evolutionary history is complex, with multiple horizontal transfers and secondary losses. One of the least recently derived, supergroup E, infects springtails (Collembola), widely distributed hexapods, with sexual and/or parthenogenetic populations depending on species. To better characterize the diversity of Wolbachia infecting springtails, the presence of Wolbachia was screened in 58 species. Eleven (20%) species were found to be positive, with three Wolbachia genotypes identified for the first time in supergroup A. The novel genotypes infect springtails ecologically and biologically different from those infected by supergroup E. To root the Wolbachia phylogeny, rather than distant other Rickettsiales, supergroup L infecting plant-parasitic nematodes was used here. We hypothesize that the ancestor of Wolbachia was consumed by soil-dwelling nematodes, and was transferred horizontally via plants into aphids, which then infected edaphic arthropods (e.g. springtails and oribatid mites) before expanding into most clades of terrestrial arthropods and filarial nematodes.
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Affiliation(s)
- Jules Rodrigues
- UMR7245, MCAM, Museum national d'Histoire naturelle, Paris, France
| | - Emilie Lefoulon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | - Benjamin Makepeace
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Coralie Martin
- UMR7245, MCAM, Museum national d'Histoire naturelle, Paris, France
| | - Cyrille A D'Haese
- UMR7179 MECADEV, Museum national d'Histoire naturelle, Paris, France
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25
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Heeren S, Maes I, Sanders M, Lye LF, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, den Broeck FV. Parasite hybridization promotes spreading of endosymbiotic viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534103. [PMID: 36993291 PMCID: PMC10055345 DOI: 10.1101/2023.03.24.534103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis parasites and their endosymbiotic Leishmania RNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.
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Affiliation(s)
- Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandy Sanders
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - James A Cotton
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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26
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Čisovská Bazsalovicsová E, Víchová B, Oboňa J, Radačovská A, Blažeková V, Králová-Hromadová I. Bird Louse Flies Ornithomya spp. (Diptera: Hippoboscidae) as Potential Vectors of Mammalian Babesia and Other Pathogens. Vector Borne Zoonotic Dis 2023; 23:275-283. [PMID: 36944122 DOI: 10.1089/vbz.2022.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Background: Birds and mammals share various ectoparasites, which are responsible for the transmission of a wide range of pathogens. The louse flies (family Hippoboscidae) are ectoparasitic dipterans feeding strictly on the blood of mammals and birds. Both sexes of the louse flies are obligatory hematophagous and are known to act as the vectors of infectious agents. Materials and Methods: A total of 20 specimens of Ornithomya sp. were collected by hand on birds caught in nets or by hand from humans in two localities in Eastern Slovakia in 2021. The DNA samples were individually screened by species-specific PCRs for the presence of selected vector-borne pathogens. Results: Taxonomic identification folowed by molecular analyses revealed two louse fly species of Ornithomya spp. (O. avicularia and O. biloba). The molecular screening provided negative PCR results for Anaplasma phagocytophilum, Borrelia burgdorferi s.l., Rickettsia spp., Bartonella spp., and Hepatozoon canis. In contrast, positive PCR results were obtained for Babesia spp., Wolbachia spp., and Trypanosoma corvi. Conclusions: Of epidemiological importance is that the louse flies can presumably spread Babesia and other pathogens by host switching which facilitates the transmission and spread of numerous pathogens.
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Affiliation(s)
| | | | - Jozef Oboňa
- Faculty of Humanities and Natural Sciences, University of Prešov, Prešov, Slovakia
| | | | - Veronika Blažeková
- Slovak Academy of Sciences, Institute of Parasitology, Košice, Slovakia
- The University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
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27
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Abstract
Insects are highly successful in colonizing a wide spectrum of ecological niches and in feeding on a wide diversity of diets. This is notably linked to their capacity to get from their microbiota any essential component lacking in the diet such as vitamins and amino acids. Over a century of research based on dietary analysis, antimicrobial treatment, gnotobiotic rearing, and culture-independent microbe detection progressively generated a wealth of information about the role of the microbiota in specific aspects of insect fitness. Thanks to the recent increase in sequencing capacities, whole-genome sequencing of a number of symbionts has facilitated tracing of biosynthesis pathways, validation of experimental data and evolutionary analyses. This field of research has generated a considerable set of data in a diversity of hosts harboring specific symbionts or nonspecific microbiota members. Here, we review the current knowledge on the involvement of the microbiota in insect and tick nutrition, with a particular focus on B vitamin provision. We specifically question if there is any specificity of B vitamin provision by symbionts compared to the redundant yet essential contribution of nonspecific microbes. We successively highlight the known aspects of microbial vitamin provision during three main life stages of invertebrates: postembryonic development, adulthood, and reproduction.
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28
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Huang C, Guo F, Wang H, Olivares J, Dalton Iii J, Belyanina O, Wattam AR, Cucinell CA, Dickerman AW, Qin QM, Han A, de Figueiredo P. An automated system for interrogating the evolution of microbial endosymbiosis. LAB ON A CHIP 2023; 23:671-683. [PMID: 36227118 DOI: 10.1039/d2lc00602b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Inter-kingdom endosymbiotic interactions between bacteria and eukaryotic cells are critical to human health and disease. However, the molecular mechanisms that drive the emergence of endosymbiosis remain obscure. Here, we describe the development of a microfluidic system, named SEER (S̲ystem for the E̲volution of E̲ndosymbiotic R̲elationships), that automates the evolutionary selection of bacteria with enhanced intracellular survival and persistence within host cells, hallmarks of endosymbiosis. Using this system, we show that a laboratory strain of Escherichia coli that initially possessed limited abilities to survive within host cells, when subjected to SEER selection, rapidly evolved to display a 55-fold enhancement in intracellular survival. Notably, molecular dissection of the evolved strains revealed that a single-point mutation in a flexible loop of CpxR, a gene regulator that controls bacterial stress responses, substantially contributed to this intracellular survival. Taken together, these results establish SEER as the first microfluidic system for investigating the evolution of endosymbiosis, show the importance of CpxR in endosymbiosis, and set the stage for evolving bespoke inter-kingdom endosymbiotic systems with novel or emergent properties.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Fengguang Guo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jasmine Olivares
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - James Dalton Iii
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Olga Belyanina
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Alice R Wattam
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Clark A Cucinell
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Allan W Dickerman
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Qing-Ming Qin
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
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29
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Mahmood S, Nováková E, Martinů J, Sychra O, Hypša V. Supergroup F Wolbachia with extremely reduced genome: transition to obligate insect symbionts. MICROBIOME 2023; 11:22. [PMID: 36750860 PMCID: PMC9903615 DOI: 10.1186/s40168-023-01462-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Wolbachia belong to highly abundant bacteria which are frequently found in invertebrate microbiomes and manifest by a broad spectrum of lifestyles from parasitism to mutualism. Wolbachia supergroup F is a particularly interesting clade as it gave rise to symbionts of both arthropods and nematodes, and some of its members are obligate mutualists. Investigations on evolutionary transitions among the different symbiotic stages have been hampered by a lack of the known diversity and genomic data for the supergroup F members. RESULTS Based on amplicon screening, short- and long-read WGS approaches, and laser confocal microscopy, we characterize five new supergroup F Wolbachia strains from four chewing lice species. These strains reached different evolutionary stages and represent two remarkably different types of symbiont genomes. Three of the genomes resemble other known members of Wolbachia F supergroup, while the other two show typical signs of ongoing gene inactivation and removal (genome size, coding density, low number of pseudogenes). Particularly, wMeur1, a symbiont fixed in microbiomes of Menacanthus eurysternus across four continents, possesses a highly reduced genome of 733,850 bp. The horizontally acquired capacity for pantothenate synthesis and localization in specialized bacteriocytes suggest its obligate nutritional role. CONCLUSIONS The genome of wMeur1 strain, from the M. eurysternus microbiome, represents the smallest currently known Wolbachia genome and the first example of Wolbachia which has completed genomic streamlining as known from the typical obligate symbionts. This points out that despite the large amount and great diversity of the known Wolbachia strains, evolutionary potential of these bacteria still remains underexplored. The diversity of the four chewing lice microbiomes indicates that this vast parasitic group may provide suitable models for further investigations. Video Abstract.
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Affiliation(s)
- Sazzad Mahmood
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, ASCR, V.V.I., České Budějovice, Czech Republic
| | - Jana Martinů
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, ASCR, V.V.I., České Budějovice, Czech Republic
| | - Oldřich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, ASCR, V.V.I., České Budějovice, Czech Republic.
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30
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Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project. PLoS Biol 2023; 21:e3001972. [PMID: 36689552 PMCID: PMC9894559 DOI: 10.1371/journal.pbio.3001972] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/02/2023] [Accepted: 12/19/2022] [Indexed: 01/24/2023] Open
Abstract
The Darwin Tree of Life (DToL) project aims to sequence all described terrestrial and aquatic eukaryotic species found in Britain and Ireland. Reference genome sequences are generated from single individuals for each target species. In addition to the target genome, sequenced samples often contain genetic material from microbiomes, endosymbionts, parasites, and other cobionts. Wolbachia endosymbiotic bacteria are found in a diversity of terrestrial arthropods and nematodes, with supergroups A and B the most common in insects. We identified and assembled 110 complete Wolbachia genomes from 93 host species spanning 92 families by filtering data from 368 insect species generated by the DToL project. From 15 infected species, we assembled more than one Wolbachia genome, including cases where individuals carried simultaneous supergroup A and B infections. Different insect orders had distinct patterns of infection, with Lepidopteran hosts mostly infected with supergroup B, while infections in Diptera and Hymenoptera were dominated by A-type Wolbachia. Other than these large-scale order-level associations, host and Wolbachia phylogenies revealed no (or very limited) cophylogeny. This points to the occurrence of frequent host switching events, including between insect orders, in the evolutionary history of the Wolbachia pandemic. While supergroup A and B genomes had distinct GC% and GC skew, and B genomes had a larger core gene set and tended to be longer, it was the abundance of copies of bacteriophage WO who was a strong determinant of Wolbachia genome size. Mining raw genome data generated for reference genome assemblies is a robust way of identifying and analysing cobiont genomes and giving greater ecological context for their hosts.
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31
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Dharamshi JE, Köstlbacher S, Schön ME, Collingro A, Ettema TJG, Horn M. Gene gain facilitated endosymbiotic evolution of Chlamydiae. Nat Microbiol 2023; 8:40-54. [PMID: 36604515 PMCID: PMC9816063 DOI: 10.1038/s41564-022-01284-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes-Verrucomicrobia-Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephan Köstlbacher
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Astrid Collingro
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria.
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32
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Schuler H, Dittmer J, Borruso L, Galli J, Fischnaller S, Anfora G, Rota‐Stabelli O, Weil T, Janik K. Investigating the microbial community of Cacopsylla spp. as potential factor in vector competence of phytoplasma. Environ Microbiol 2022; 24:4771-4786. [PMID: 35876309 PMCID: PMC9804460 DOI: 10.1111/1462-2920.16138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 01/05/2023]
Abstract
Phytoplasmas are obligatory intracellular bacteria that colonize the phloem of many plant species and cause hundreds of plant diseases worldwide. In nature, phytoplasmas are primarily transmitted by hemipteran vectors. While all phloem-feeding insects could in principle transmit phytoplasmas, only a limited number of species have been confirmed as vectors. Knowledge about factors that might determine the vector capacity is currently scarce. Here, we characterized the microbiomes of vector and non-vector species of apple proliferation (AP) phytoplasma 'Candidatus Phytoplasma mali' to investigate their potential role in the vector capacity of the host. We performed high-throughput 16S rRNA metabarcoding of the two principal AP-vectors Cacopsylla picta and Cacopsylla melanoneura and eight Cacopsylla species, which are not AP-vectors but co-occur in apple orchards. The microbiomes of all species are dominated by Carsonella, the primary endosymbiont of psyllids and a second uncharacterized Enterobacteriaceae endosymbiont. Each Cacopsylla species harboured a species-specific phylotype of both symbionts. Moreover, we investigated differences between the microbiomes of AP-vector versus non-vector species and identified the predominant endosymbionts but also Wolbachia and several minor taxa as potential indicator species. Our study highlights the importance of considering the microbiome in future investigations of potential factors influencing host vector competence. We investigated the potential role of symbiotic bacteria in the acquisition and transmission of phytoplasma. By comparing the two main psyillid vector species of Apple proliferation (AP) phytoplasma and eight co-occurring species, which are not able to vector AP-phytoplasma, we found differences in the microbial communities of AP-vector and non-vector species, which appear to be driven by the predominant symbionts in both vector species and Wolbachia and several minor taxa in the non-vector species. In contrast, infection with AP-phytoplasma did not affect microbiome composition in both vector species. Our study provides new insights into the endosymbiont diversity of Cacopsylla spp. and highlights the importance of considering the microbiome when investigating potential factors influencing host vector competence.
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Affiliation(s)
- Hannes Schuler
- Faculty of Science and TechnologyFree University of Bozen‐BolzanoBozen‐BolzanoItaly,Competence Centre for Plant HealthFree University of Bozen‐BolzanoBozen‐BolzanoItaly
| | - Jessica Dittmer
- Faculty of Science and TechnologyFree University of Bozen‐BolzanoBozen‐BolzanoItaly,Université d'Angers, Institut Agro, INRAE, IRHS, SFR QuasavAngersFrance
| | - Luigimaria Borruso
- Faculty of Science and TechnologyFree University of Bozen‐BolzanoBozen‐BolzanoItaly
| | - Jonas Galli
- Department of Forest and Soil Sciences, BOKUUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | | | - Gianfranco Anfora
- Research and Innovation CenterFondazione Edmund MachSan Michele all'AdigeItaly,Center Agriculture Food EnvironmentUniversity of TrentoSan Michele all'AdigeItaly
| | - Omar Rota‐Stabelli
- Research and Innovation CenterFondazione Edmund MachSan Michele all'AdigeItaly,Center Agriculture Food EnvironmentUniversity of TrentoSan Michele all'AdigeItaly
| | - Tobias Weil
- Research and Innovation CenterFondazione Edmund MachSan Michele all'AdigeItaly
| | - Katrin Janik
- Center Agriculture Food EnvironmentUniversity of TrentoSan Michele all'AdigeItaly
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Shastry V, Bell KL, Buerkle CA, Fordyce JA, Forister ML, Gompert Z, Lebeis SL, Lucas LK, Marion ZH, Nice CC. A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics. G3 GENES|GENOMES|GENETICS 2022; 12:6670626. [PMID: 35976120 PMCID: PMC9526071 DOI: 10.1093/g3journal/jkac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022]
Abstract
Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only 5 sequence reads per host individual. Using this threshold, we detected Wolbachia in all but 2 of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0% to 100% of individuals, but with most localities having high infection frequencies (mean = 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent 3 separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other 2 strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the 2 most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in Lycaeides melissa and haplotype A2 observed most often in Lycaeides idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than 1 major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.
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Affiliation(s)
- Vivaswat Shastry
- Committee on Genetics, Genomics and Systems Biology, University of Chicago , Chicago, IL 60637, USA
| | - Katherine L Bell
- Department of Biology, University of Nevada , Reno, NV 89557, USA
| | - C Alex Buerkle
- Department of Botany, University of Wyoming , Laramie, WY 82071, USA
| | - James A Fordyce
- Department of Ecology & Evolutionary Biology, University of Tennessee , Knoxville, TN 37996, USA
| | | | | | - Sarah L Lebeis
- Department of Microbiology & Molecular Genetics, Michigan State University , East Lansing, MI 48824, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University , Logan, UT 84322, USA
| | - Zach H Marion
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury , Christchurch, New Zealand
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology, Texas State University , San Marcos, TX 78666, USA
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Martinez J, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Sinkins SP. Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genet 2022; 18:e1010406. [PMID: 36121852 PMCID: PMC9560607 DOI: 10.1371/journal.pgen.1010406] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/13/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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35
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Romero Picazo D, Werner A, Dagan T, Kupczok A. Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance. Genome Biol Evol 2022; 14:evac098. [PMID: 35731940 PMCID: PMC9260185 DOI: 10.1093/gbe/evac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.
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Affiliation(s)
- Devani Romero Picazo
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Almut Werner
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Bioinformatics Group, Wageningen University & Research, 6708PB Wageningen, The Netherlands
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Shigenobu S. Editorial overview: Insect genomics: Genomics of emerging model insects. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100913. [PMID: 35331977 DOI: 10.1016/j.cois.2022.100913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Shuji Shigenobu
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
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37
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Strunov A, Lerch S, Blanckenhorn WU, Miller WJ, Kapun M. Complex effects of environment and Wolbachia infections on the life history of Drosophila melanogaster hosts. J Evol Biol 2022; 35:788-802. [PMID: 35532932 PMCID: PMC9321091 DOI: 10.1111/jeb.14016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022]
Abstract
Wolbachia bacteria are common endosymbionts of many arthropods found in gonads and various somatic tissues. They manipulate host reproduction to enhance their transmission and confer complex effects on fitness-related traits. Some of these effects can serve to increase the survival and transmission efficiency of Wolbachia in the host population. The Wolbachia-Drosophila melanogaster system represents a powerful model to study the evolutionary dynamics of host-microbe interactions and infections. Over the past decades, there has been a replacement of the ancestral wMelCS Wolbachia variant by the more recent wMel variant in worldwide D. melanogaster populations, but the reasons remain unknown. To investigate how environmental change and genetic variation of the symbiont affect host developmental and adult life-history traits, we compared effects of both Wolbachia variants and uninfected controls in wild-caught D. melanogaster strains at three developmental temperatures. While Wolbachia did not influence any developmental life-history traits, we found that both lifespan and fecundity of host females were increased without apparent fitness trade-offs. Interestingly, wMelCS-infected flies were more fecund than uninfected and wMel-infected flies. By contrast, males infected with wMel died sooner, indicating sex-specific effects of infection that are specific to the Wolbachia variant. Our study uncovered complex temperature-specific effects of Wolbachia infections, which suggests that symbiont-host interactions in nature are strongly dependent on the genotypes of both partners and the thermal environment.
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Affiliation(s)
- Anton Strunov
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Sina Lerch
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Wolfgang J. Miller
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of Cell and Developmental BiologyCenter for Anatomy and Cell BiologyMedical University of ViennaWienAustria
- Natural History Museum of ViennaWienAustria
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38
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Gomes TMFF, Wallau GL, Loreto ELS. Multiple long-range host shifts of major Wolbachia supergroups infecting arthropods. Sci Rep 2022; 12:8131. [PMID: 35581290 PMCID: PMC9114371 DOI: 10.1038/s41598-022-12299-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Wolbachia is a genus of intracellular bacterial endosymbionts found in 20–66% of all insect species and a range of other invertebrates. It is classified as a single species, Wolbachia pipientis, divided into supergroups A to U, with supergroups A and B infecting arthropods exclusively. Wolbachia is transmitted mainly via vertical transmission through female oocytes, but can also be transmitted across different taxa by host shift (HS): the direct transmission of Wolbachia cells between organisms without involving vertically transmitted gametic cells. To assess the HS contribution, we recovered 50 orthologous genes from over 1000 Wolbachia genomes, reconstructed their phylogeny and calculated gene similarity. Of 15 supergroup A Wolbachia lineages, 10 have similarities ranging from 95 to 99.9%, while their hosts’ similarities are around 60 to 80%. For supergroup B, four out of eight lineages, which infect diverse and distantly-related organisms such as Acari, Hemiptera and Diptera, showed similarities from 93 to 97%. These results show that Wolbachia genomes have a much higher similarity when compared to their hosts’ genes, which is a major indicator of HS. Our comparative genomic analysis suggests that, at least for supergroups A and B, HS is more frequent than expected, occurring even between distantly-related species.
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Affiliation(s)
- Tiago M F F Gomes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel L Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Elgion L S Loreto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. .,Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil. .,Biochemistry and Molecular Biology Department, Federal University of Santa Maria, Av. Roraima 1000, Santa Maria, RS, CEP 97105.900, Brazil.
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39
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Weyandt N, Aghdam SA, Brown AMV. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. Front Microbiol 2022; 13:867392. [PMID: 35547116 PMCID: PMC9084900 DOI: 10.3389/fmicb.2022.867392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.
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Affiliation(s)
- Nicholas Weyandt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Shiva A Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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40
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Quek S, Cerdeira L, Jeffries CL, Tomlinson S, Walker T, Hughes GL, Heinz E. Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements. Microb Genom 2022; 8. [PMID: 35446252 PMCID: PMC9453072 DOI: 10.1099/mgen.0.000805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wolbachia is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, Wolbachia pipientis, divided into several ‘supergroups’ based on multilocus sequence typing. Wolbachia strains in mosquitoes have been shown to inhibit the transmission of human pathogens, including Plasmodium malaria parasites and arboviruses. Despite their large host range, Wolbachia strains within the major malaria vectors of the Anopheles gambiae and Anopheles funestus complexes appear at low density, established solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B Wolbachia within Anopheles demeilloni and Anopheles moucheti has opened exciting possibilities to explore naturally occurring Wolbachia endosymbionts in Anopheles for biocontrol strategies to block Plasmodium transmission. Here, we utilize genomic analyses to demonstrate that both Wolbachia strains have retained all key metabolic and transport pathways despite their smaller genome size, with this reduction potentially attributable to degenerated prophage regions. Even with this reduction, we confirmed the presence of cytoplasmic incompatibility (CI) factor genes within both strains, with wAnD maintaining intact copies of these genes while the cifB gene was interrupted in wAnM, so functional analysis is required to determine whether wAnM can induce CI. Additionally, phylogenetic analysis indicates that these Wolbachia strains may have been introduced into these two Anopheles species via horizontal transmission events, rather than by ancestral acquisition and subsequent loss events in the Anopheles gambiae species complex. These are the first Wolbachia genomes, to our knowledge, that enable us to study the relationship between natural strain Plasmodium malaria parasites and their anopheline hosts.
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Affiliation(s)
- Shannon Quek
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Louise Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claire L Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Sean Tomlinson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Grant L Hughes
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Yang Q, Chung J, Robinson KL, Schmidt TL, Ross PA, Liang J, Hoffmann AA. Sex-specific distribution and classification of Wolbachia infections and mitochondrial DNA haplogroups in Aedes albopictus from the Indo-Pacific. PLoS Negl Trop Dis 2022; 16:e0010139. [PMID: 35417447 PMCID: PMC9037918 DOI: 10.1371/journal.pntd.0010139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
The arbovirus vector Aedes albopictus (Asian tiger mosquito) is common throughout the Indo-Pacific region, where most global dengue transmission occurs. We analysed population genomic data and tested for cryptic species in 160 Ae. albopictus sampled from 16 locations across this region. We found no evidence of cryptic Ae. albopictus but found multiple intraspecific COI haplotypes partitioned into groups representing three Asian lineages: East Asia, Southeast Asia and Indonesia. Papua New Guinea (PNG), Vanuatu and Christmas Island shared recent coancestry, and Indonesia and Timor-Leste were likely invaded from East Asia. We used a machine learning trained on morphologically sexed samples to classify sexes using multiple genetic features and then characterized the wAlbA and wAlbB Wolbachia infections in 664 other samples. The wAlbA and wAlbB infections as detected by qPCR showed markedly different patterns in the sexes. For females, most populations had a very high double infection incidence, with 67% being the lowest value (from Timor-Leste). For males, the incidence of double infections ranged from 100% (PNG) to 0% (Vanuatu). Only 6 females were infected solely by the wAlbA infection, while rare uninfected mosquitoes were found in both sexes. The wAlbA and wAlbB densities varied significantly among populations. For mosquitoes from Torres Strait and Vietnam, the wAlbB density was similar in single-infected and superinfected (wAlbA and wAlbB) mosquitoes. There was a positive association between wAlbA and wAlbB infection densities in superinfected Ae. albopictus. Our findings provide no evidence of cryptic species of Ae. albopictus in the region and suggest site-specific factors influencing the incidence of Wolbachia infections and their densities. We also demonstrate the usefulness of ddRAD tag depths as sex-specific mosquito markers. The results provide baseline data for the exploitation of Wolbachia-induced cytoplasmic incompatibility (CI) in dengue control. The mosquito Aedes albopictus transmits dengue and other arboviruses. This study investigates the genetics of these mosquitoes and their endosymbiont Wolbachia in the Indo-Pacific region, where 70% of global dengue transmission occurs. The analysis of mitochondrial DNA sequences showed no evidence of cryptic Ae. albopictus but suggested three Asian lineages: East Asia, Southeast Asia and Indonesia. Papua New Guinea, Vanuatu and Christmas Island shared recent coancestry, and Indonesia and Timor-Leste were likely invaded from East Asia. We used bioinformatics to classify sexes and then characterized the wAlbA and wAlbB Wolbachia infections via both bioinformatics and quantitative PCR. We found markedly different patterns of wAlbA and wAlbB infections in the sexes. The wAlbA and wAlbB densities varied significantly among populations, suggesting site-specific factors influencing the incidence of Wolbachia infections and their densities. We also demonstrate the usefulness of next generation sequencing data in developing molecular markers that can be repeatedly reanalysed to investigate new issues as these arise. These results provide baseline data for the exploitation of Wolbachia-induced cytoplasmic incompatibility in dengue control.
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Affiliation(s)
- Qiong Yang
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
- * E-mail: (QY); (AAH)
| | - Jessica Chung
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia
| | - Katie L. Robinson
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Thomas L. Schmidt
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Perran A. Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Jiaxin Liang
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Australia
- * E-mail: (QY); (AAH)
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Namias A, Sicard M, Weill M, Charlat S. From Wolbachia genomics to phenotype: molecular models of cytoplasmic incompatibility must account for the multiplicity of compatibility types. CURRENT OPINION IN INSECT SCIENCE 2022; 49:78-84. [PMID: 34954414 DOI: 10.1016/j.cois.2021.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/22/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Wolbachia endosymbionts commonly induce cytoplasmic incompatibility, making infected males' sperm lethal to the embryos unless these are rescued by the same bacterium, inherited from their mother. Causal genes were recently identified but two families of mechanistic models are still opposed. In the toxin-antidote model, interaction between the toxin and the antidote is required for rescuing the embryos. In host modification models, a host factor is misregulated in sperm and rescue occurs through compensation or withdrawal of this modification. While these models have been thoroughly discussed, the multiplicity of compatibility types, that is, the existence of many mutually incompatible strains, as seen in Culex mosquitoes, has not received sufficient attention. To explain such a fact, host modification models must posit that the same embryonic defects can be induced and rescued through a large variety of host targets. Conversely, the toxin-antidote model simply accommodates this pattern in a lock-key fashion, through variations in the toxin-antidote interaction sites.
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Affiliation(s)
- Alice Namias
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Mylène Weill
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Sylvain Charlat
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622, France.
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43
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Konecka E. Fifty shades of bacterial endosymbionts and some of them still remain a mystery: Wolbachia and Cardinium in oribatid mites (Acari: Oribatida). J Invertebr Pathol 2022; 189:107733. [DOI: 10.1016/j.jip.2022.107733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/28/2022]
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44
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Narrow Genetic Diversity of Wolbachia Symbionts in Acrididae Grasshopper Hosts (Insecta, Orthoptera). Int J Mol Sci 2022; 23:ijms23020853. [PMID: 35055035 PMCID: PMC8775660 DOI: 10.3390/ijms23020853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 01/27/2023] Open
Abstract
Bacteria of the Wolbachia genus are maternally inherited symbionts of Nematoda and numerous Arthropoda hosts. There are approximately 20 lineages of Wolbachia, which are called supergroups, and they are designated alphabetically. Wolbachia strains of the supergroups A and B are predominant in arthropods, especially in insects, and supergroup F seems to rank third. Host taxa have been studied very unevenly for Wolbachia symbionts, and here, we turn to one of largely unexplored insect families: Acrididae. On the basis of five genes subject to multilocus sequence typing, we investigated the incidence and genetic diversity of Wolbachia in 41 species belonging three subfamilies (Gomphocerinae, Oedipodinae, and Podisminae) collected in Turkey, Kazakhstan, Tajikistan, Russia, and Japan, making 501 specimens in total. Our results revealed a high incidence and very narrow genetic diversity of Wolbachia. Although only the strains belonging to supergroups A and B are commonly present in present, the Acrididae hosts here proved to be infected with supergroups B and F without A-supergroup variants. The only trace of an A-supergroup lineage was noted in one case of an inter-supergroup recombinant haplotype, where the ftsZ gene came from supergroup A, and the others from supergroup B. Variation in the Wolbachia haplotypes in Acrididae hosts within supergroups B and F was extremely low. A comprehensive genetic analysis of Wolbachia diversity confirmed specific features of the Wolbachia allelic set in Acrididae hosts. This result can help to elucidate the crucial issue of Wolbachia biology: the route(s) and mechanism(s) of Wolbachia horizontal transmission.
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45
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Sanaei E, Lin YP, Cook LG, Engelstädter J. Wolbachia in scale insects: a distinct pattern of infection frequencies and potential transfer routes via ant associates. Environ Microbiol 2021; 24:1326-1339. [PMID: 34792280 DOI: 10.1111/1462-2920.15833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/05/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
Wolbachia is one of the most successful endosymbiotic bacteria of arthropods. Known as the 'master of manipulation', Wolbachia can induce a wide range of phenotypes in its host that can have far-reaching ecological and evolutionary consequences and may be exploited for disease and pest control. However, our knowledge of Wolbachia's distribution and the infection rate is unevenly distributed across arthropod groups such as scale insects. We fitted a distribution of within-species prevalence of Wolbachia to our data and compared it to distributions fitted to an up-to-date dataset compiled from surveys across all arthropods. The estimated distribution parameters indicate a Wolbachia infection frequency of 43.6% (at a 10% prevalence threshold) in scale insects. Prevalence of Wolbachia in scale insects follows a distribution similar to exponential decline (most species are predicted to have low prevalence infections), in contrast to the U-shaped distribution estimated for other taxa (most species have a very low or very high prevalence). We observed no significant associations between Wolbachia infection and scale insect traits. Finally, we screened for Wolbachia in scale insect's ecological associates. We found a positive correlation between Wolbachia infection in scale insects and their ant associates, pointing to a possible route of horizontal transfer of Wolbachia.
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Affiliation(s)
- Ehsan Sanaei
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Yen-Po Lin
- Department of Plant Medicine, College of Agriculture, National Chiayi University, Chiayi City, 60004, Taiwan
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
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46
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Wittmeyer KT, Oppenheim SJ, Hopper KR. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage. G3 (BETHESDA, MD.) 2021; 12:6423991. [PMID: 34751385 PMCID: PMC8727961 DOI: 10.1093/g3journal/jkab386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis made with Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies of A. atriplicis differed in contiguity, and the meta-assembly of these assemblies was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly to the point where it was also at the chromosomal-level. However, completeness of the A. atriplicis assembly, as measured by percent complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportions with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by percent complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggest greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.
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Affiliation(s)
- Kameron T Wittmeyer
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA
| | | | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA,Corresponding author: USDA-ARS, Beneficial Insect Introductions Research Unit, 501 South Chapel Street, Newark, DE 19713, USA.
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47
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Ortiz-Baez AS, Shi M, Hoffmann AA, Holmes EC. RNA virome diversity and Wolbachia infection in individual Drosophila simulans flies. J Gen Virol 2021; 102. [PMID: 34704919 PMCID: PMC8604192 DOI: 10.1099/jgv.0.001639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The endosymbiont bacteria of the genus Wolbachia are associated with multiple mutualistic effects on insect biology, including nutritional and antiviral properties. Members of the genus Wolbachia naturally occur in fly species of the genus Drosophila, providing an operational model host for studying how virome composition may be affected by its presence. Drosophila simulans populations can carry a variety of strains of members of the genus Wolbachia, with the wAu strain associated with strong antiviral protection under experimental conditions. We used D. simulans sampled from the Perth Hills, Western Australia, to investigate the potential virus protective effect of the wAu strain of Wolbachia on individual wild-caught flies. Our data revealed no appreciable variation in virus composition and abundance between individuals infected or uninfected with Wolbachia associated with the presence or absence of wAu. However, it remains unclear whether wAu might affect viral infection and host survival by increasing tolerance rather than inducing complete resistance. These data also provide new insights into the natural virome diversity of D. simulans. Despite the small number of individuals sampled, we identified a repertoire of RNA viruses, including nora virus, galbut virus, thika virus and La Jolla virus, that have been identified in other species of the genus Drosophila. Chaq virus-like sequences associated with galbut virus were also detected. In addition, we identified five novel viruses from the families Reoviridae, Tombusviridae, Mitoviridae and Bunyaviridae. Overall, this study highlights the complex interaction between Wolbachia and RNA virus infections and provides a baseline description of the natural virome of D. simulans.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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48
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Fenton A, Camus MF, Hurst GDD. Positive selection on mitochondria may eliminate heritable microbes from arthropod populations. Proc Biol Sci 2021; 288:20211735. [PMID: 34583583 PMCID: PMC8488761 DOI: 10.1098/rspb.2021.1735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Diverse eukaryotic taxa carry facultative heritable symbionts, microbes that are passed from mother to offspring. These symbionts are coinherited with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria, but with currently unknown consequences for symbiont evolution. We therefore employed a population genetic mean field framework to model the impact of selection on mitochondrial DNA (mtDNA) upon symbiont frequency for three generic scenarios of host–symbiont interaction. Our models predict that direct selection on mtDNA can drive symbionts out of the population where a positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, by contrast, the positively selected mtDNA mutation occurs in a symbiont-infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. We conclude that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA.
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Affiliation(s)
- Andy Fenton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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49
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Perreau J, Moran NA. Genetic innovations in animal-microbe symbioses. Nat Rev Genet 2021; 23:23-39. [PMID: 34389828 DOI: 10.1038/s41576-021-00395-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Animal hosts have initiated myriad symbiotic associations with microorganisms and often have maintained these symbioses for millions of years, spanning drastic changes in ecological conditions and lifestyles. The establishment and persistence of these relationships require genetic innovations on the parts of both symbionts and hosts. The nature of symbiont innovations depends on their genetic population structure, categorized here as open, closed or mixed. These categories reflect modes of inter-host transmission that result in distinct genomic features, or genomic syndromes, in symbionts. Although less studied, hosts also innovate in order to preserve and control symbiotic partnerships. New capabilities to sequence host-associated microbial communities and to experimentally manipulate both hosts and symbionts are providing unprecedented insights into how genetic innovations arise under different symbiont population structures and how these innovations function to support symbiotic relationships.
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Affiliation(s)
- Julie Perreau
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
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50
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Shropshire JD, Rosenberg R, Bordenstein SR. The impacts of cytoplasmic incompatibility factor (cifA and cifB) genetic variation on phenotypes. Genetics 2021; 217:1-13. [PMID: 33683351 PMCID: PMC8218869 DOI: 10.1093/genetics/iyaa007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Wolbachia are maternally transmitted, intracellular bacteria that can
often selfishly spread through arthropod populations via cytoplasmic incompatibility (CI).
CI manifests as embryonic death when males expressing prophage WO genes
cifA and cifB mate with uninfected females or females
harboring an incompatible Wolbachia strain. Females with a compatible
cifA-expressing strain rescue CI. Thus, cif-mediated
CI confers a relative fitness advantage to females transmitting
Wolbachia. However, whether cif sequence variation
underpins incompatibilities between Wolbachia strains and variation in CI
penetrance remains unknown. Here, we engineer Drosophila melanogaster to
transgenically express cognate and non-cognate cif homologs and assess
their CI and rescue capability. Cognate expression revealed that cifA;B
native to D. melanogaster causes strong CI, and cognate
cifA;B homologs from two other Drosophila-associated
Wolbachia cause weak transgenic CI, including the first demonstration
of phylogenetic type 2 cifA;B CI. Intriguingly, non-cognate expression of
cifA and cifB alleles from different strains revealed
that cifA homologs generally contribute to strong transgenic CI and
interchangeable rescue despite their evolutionary divergence, and cifB
genetic divergence contributes to weak or no transgenic CI. Finally, we find that a type 1
cifA can rescue CI caused by a genetically divergent type 2
cifA;B in a manner consistent with unidirectional incompatibility. By
genetically dissecting individual CI functions for type 1 and 2 cifA and
cifB, this work illuminates new relationships between
cif genotype and CI phenotype. We discuss the relevance of these
findings to CI’s genetic basis, phenotypic variation patterns, and mechanism.
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Affiliation(s)
- J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA.,Vanderbilt Microbiome Initiative, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA.,Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Rachel Rosenberg
- Department of Biological Sciences, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA.,Vanderbilt Microbiome Initiative, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA.,Vanderbilt Microbiome Initiative, Vanderbilt University, VU Station B, Box 35-1634, Nashville, TN 37235, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37235, USA.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37235, USA
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